Abstract
Recently, an alternative strategy for the parallelization of molecular dynamics simulations with short-ranged forces has been proposed. In this work, this algorithm is tested on a variety of multi-core systems using three types of benchmark simulations. The results show that the new algorithm gives consistent speedups which are depending on the properties of the simulated system either comparable or superior to those obtained with spatial decomposition. Comparisons of the parallel speedup on different systems indicates that on multi-core machines the parallel efficiency of the method is mainly limited by memory access speed.
Highlights
Molecular dynamics (MD) is a particle based simulation technique that is widely used in many areas of computational science [1, 2, 3]
Benchmark Systems In order to test the e ciency of the cell task method, three types of benchmark simulations have been repeated on a variety of multi-core systems
Load imbalances occur in this system only if the spatial decomposition is incommensurable with the number of lattice planes
Summary
Molecular dynamics (MD) is a particle based simulation technique that is widely used in many areas of computational science [1, 2, 3]. In this article the e ciency of the cell task method is tested on a variety of di↵erent multi-core systems. Benchmark Systems In order to test the e ciency of the cell task method, three types of benchmark simulations have been repeated on a variety of multi-core systems.
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